HIGH GC CONTENTS OF PRIMER 5′-END INCREASES REACTION EFFICIENCY IN POLYMERASE CHAIN REACTION

被引：6

作者：

Shinoda, Naoki ^{[1
]}

Yoshida, Tomotaro

Kusama, Toyoko

Takagi, Masami

Hayakawa, Toshiaki

Onodera, Takashi ^{[2
]}

Sugiura, Katsuaki

机构：

[1] Food & Agr Mat Inspect Ctr, Chuo Ku, Saitama 3309731, Japan

[2] Univ Tokyo, Dept Mol Immunol, Sch Agr & Life Sci, Tokyo, Japan

来源：

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS | 2009年 / 28卷 / 04期

关键词：

Polymerase chain reaction; primer sequence; amplification efficiency; RUMINANT FEED; DNA; PCR; DESIGN; IDENTIFICATION; AMPLIFICATION; SUCCESS; MEAT;

D O I：

10.1080/15257770902963400

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Many studies have suggested that regulation of the polymerase chain reaction (PCR) is influenced. by several factors. However, the understanding of reaction efficiency factors is not sufficient. Here we propose that high GC contents of primer 5'-end increases reaction efficiency in PCR. Using 71 primers (45 pairs), we analyzed factors that affect reaction efficiency, and statistically tested. the correlation between the aniplification signals and several factors. As a result, there were significant correlations between the amplification signals and the GC contents in the first 1 similar to 3 bps of primer 5'-end.

引用

页码：324 / 330

页数：7

共 19 条

[1] Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms
Adessi, Celine
Matton, Gilles
Ayala, Guidon
Turcatti, Gerardo
Mermod, Jean-Jacques
Mayer, Pascal
Kawashima, Eric
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (20) : 87
[2] Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder
Afonina, I
Zivarts, M
Kutyavin, I
Lukhtanov, E
Gamper, H
Meyer, RB
[J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (13) : 2657 - 2660
[3] Predicting failure rate of PCR in large genomes
Andreson, Reidar
Mols, Tonu
Remm, Maido
[J]. NUCLEIC ACIDS RESEARCH, 2008, 36 (11)
[4] Regionalized GC content of template DNA as a predictor of PCR success
Benita, Y
Oosting, RS
Lok, MC
Wise, MJ
Humphery-Smith, I
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (16)
[5] A competitive polymerase chain reaction-based approach for the identification and semiquantification of mitochondrial DNA in differently heat-treated bovine meat and bone meal
Frezza, D
Favaro, M
Vaccari, G
von-Holst, C
Giambra, V
Anklam, E
Bove, D
Battaglia, PA
Agrimi, U
Brambilla, G
Ajmone-Marsan, P
Tartaglia, M
[J]. JOURNAL OF FOOD PROTECTION, 2003, 66 (01) : 103 - 109
[6] Primer design for large scale sequencing
Haas, S
Vingron, M
Poustka, A
Wiemann, S
[J]. NUCLEIC ACIDS RESEARCH, 1998, 26 (12) : 3006 - 3012
[7] Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs
Housley, Donna J. E.
Zalewski, Zachary A.
Beckett, Stephanie E.
Venta, Patrick J.
[J]. BMC GENOMICS, 2006, 7 (1)
[8] Development of primers for detection of meat and bone meal in ruminant feed and identification of the animal of origin
Kusama, T
Nomura, T
Kadowaki, K
[J]. JOURNAL OF FOOD PROTECTION, 2004, 67 (06) : 1289 - 1292
[9] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3′-end subsequences
Miura, F
Uematsu, C
Sakaki, Y
Ito, T
[J]. BIOINFORMATICS, 2005, 21 (24) : 4363 - 4370
[10] MULLIS KB, 1987, METHOD ENZYMOL, V155, P335

← 1 2 →